[BioC] MAS 5.0

[Wilkinson, Mark]

This issue in general has kept me somewhat reluctant to use the affy
package.

To the affy package authors:  is the idea for affy to reproduce the
functionality of MAS 5.0 (at least for some parts)?  In other words, should
I be able to do probe level summaries exactly like MAS5, or is affy's
version just a close approximation?



Mark Wilkinson
Informatics Analyst
St. Jude Children's Research Hospital
Department of Pharmaceutical Sciences

The opinions expressed here are my own and do not necessarily represent
those of St. Jude Children's Research Hospital.


 -----Original Message-----
From: 	Helene Boucher [mailto:bouhel01@borabora.crchul.ulaval.ca] 
Sent:	Wednesday, January 22, 2003 10:09 AM
To:	bioconductor@stat.math.ethz.ch
Subject:	[BioC] MAS 5.0



I tried  expresso  to reproduce expression measures from MAS 5.0 but I get a
slight 
difference from Affymetrix as illustrated on a set of 3 chips for selected
probe 
sets. Any idea why that is?  The version of Unix we have is SunOS Release
5.8.

Thanks,

Helene


100001_at       29.6222834908728        10.2880336221679
80.7973366171763
100002_at       9.94107964466495        62.9653009129815
53.7356175596969
100003_at       2262.85860839992        1539.08193903367
1910.0212276237
100004_at       305.100816246875        188.181043441888
239.902666074234
100005_at       434.482366404616        638.860562906946
589.86003783735
100006_at       61.9587790672468        32.9005081415387
61.5914892307955
100007_at       890.772109484179        988.46987085589 1076.17589775836
100009_r_at     89.4108950323307        46.1650654835421
54.0252748779586
100010_at       227.251880233698        401.164278682326
424.746403324436
100011_at       1157.66237359318        702.613181714498
882.033123210299
100012_at       893.256638440421        1511.96440725101
2054.18415149103
----------------------------------------------------------------------------
--------
 

100001_at       16      16      26.0    A       0.781017

 

100002_at       16      16      10.2    A       0.910595

 

100003_at       16      16      2271.8  P       0.000219

 

100004_at       16      16      302.2   P       0.004863

 

100005_at       16      16      439.1   P       0.006532

 

100006_at       16      16      63.5    A       0.358690

 

100007_at       16      16      894.7   P       0.001354

 

100009_r_at     16      16      90.2    P       0.000805

 

100010_at       16      16      227.4   P       0.009985
----------------------------------------------------------------------------
---------
100001_at       16      16      11.0    A       0.602006

 

100002_at       16      16      58.8    A       0.438361

 

100003_at       16      16      1545.5  P       0.000219

 

100004_at       16      16      191.7   P       0.011447

 

100005_at       16      16      641.4   P       0.002617

 

100006_at       16      16      33.7    A       0.117160

 

100007_at       16      16      992.9   P       0.001141

 

100009_r_at     16      16      47.4    P       0.011447

 

100010_at       16      16      402.6   P       0.001354
----------------------------------------------------------------------------
---------
100001_at       16      16      81.1    A       0.438361

 

100002_at       16      16      44.4    A       0.581931

 

100003_at       16      16      1917.2  P       0.000219

 

100004_at       16      16      244.2   P       0.031336

 

100005_at       16      16      591.0   P       0.001354

 

100006_at       16      16      62.9    A       0.089405

 

100007_at       16      16      1080.6  P       0.000673

 

100009_r_at     16      16      54.5    P       0.011447

 

100010_at       16      16      428.1   P       0.000959
----------------------------------------------------------------------------
--------

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